A)
grep '^@' test.fastq |wc -l (or) wc -l test.fastq (and then divide by 4)
B)
cp /corral-repl/utexas/BioITeam/rnaseq_course/C .
C)
grep 'ACTACCGATCCA' test.fastq |wc -l
D)
module load fastx_toolkit
fastx_clipper -a ACTACCGATCCA -i test.fastq -o <outputfile> -l <discardSeqsShorterThanN>
E) module load cufflinks
nano commands.cufflinks
cufflinks -p 2 -g genes.formatted.gtf -o <output> test.bam
module load python
launcher_creator.py -n cufflinks -t 01:00:00 -j commands.cufflinks -q development -a CCBB
qsub launcher_creator.py